In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

Nat Rev Microbiol. 2011 Jan;9(1):39-50. doi: 10.1038/nrmicro2456. Epub 2010 Dec 6.


There is a wide diversity of unexplored metabolism encoded in the genomes of microorganisms that have an important environmental role. Genome-scale metabolic modelling enables the individual reactions that are encoded in annotated genomes to be organized into a coherent whole, which can then be used to predict metabolic fluxes that will optimize cell function under a range of conditions. In this Review, we summarize a series of studies in which genome-scale metabolic modelling of Geobacter spp. has resulted in an in-depth understanding of their central metabolism and ecology. A similar iterative modelling and experimental approach could accelerate elucidation of the physiology and ecology of other microorganisms inhabiting a diversity of environments, and could guide optimization of the practical applications of these species.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Computer Simulation*
  • Environment*
  • Gene Expression Regulation, Bacterial / physiology
  • Genome, Bacterial*
  • Geobacter / genetics*
  • Geobacter / metabolism*
  • Models, Biological*